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• Can't use cached bed file
  Hey, I wanted to have built-in BED files specific to the genome references that I added to my lo...
• Get Count of lines in a BED data file
  I simply want to get a count of rows in a Galaxy output BED file (in this case the number of gene...
• Peak Calling on BED files
  This is somewhat of a naive question. I've been using MACS2 on galaxy to call peaks on my ChIP-s...
• Bed To Bam Conversion In Galaxy
  Is it possible to use some tool in Galaxy to convert BED file to Bam/ sam file. In other word do ...
• Gro-Seq! And Galaxy
  Hi all, I have BED and WIG files from Gro-Seq but Galaxy did not recognize these files. WHY is t...
• Liftover tool not working at UCSC
  Hello, I tried to convert hg18 coordinates in a BED format data with UCSC liftover and it is not...
• Profile annotation No table available
  Dear all, I have a bed file not annotated, and I would like to use the Operate on genomic interv...
• Bed To Gff
  Dear Galaxy I have a problem converting Interval to GFF. I used the tool BED-to- GFFconverter. ...
• There is a link to view human hg19 but not hg38 bed files using UCSC. Why?
  I am working my way through the Galaxy 101 tutorial. When I use hg19 data I have the option of vi...
• Galaxy: Genomic Intervals to strict BED Conversion
  Hello: I'm new to the forum and Galaxy/bioinformatics. In the last two months I've been followi...
• Converting File To Interval Or Bed In A Workflow
  Dear Galaxy users/developers, I was wondering if anyone knows a way to take a tabular file (i.e....
• You are not allowed to access this dataset
  Hello everyone ! I have a strange behaviour on my histories and it is troublesome since it affe...
• Orthologus Regions
  Hi,       I have a bed file for the chimp genome and I want to download the same region for the ...
• bed file to bigwig file conversion
  Hello there, I want to convert my bed files to bigwig files in order to visualize them using IGV...
• FastQ to annotated MACS Peaks
  Hello I'm a Ms Student, and I'm am completely new to galaxy. Since 4 days I'm am trying to lear...
• Chip-Seq And Gene Ontology With Galaxy-Ucsc
  Hi, I am currently doing some ChIP-Seq experiments, to analyze the data I get from the PeakFinde...
• Filtering using BED file
  I have generated mpileups and I wish to filter the desired variants using a BED file. I have done...
• Fwd: Exome Sequencing Analysis
  Hello, My name is Johnathan Cooper-Knock, I am a clinical fellow based at the University of Shef...
• Give a list of genes and return Transcription starting sites as a bed file
  Dear there: I have a questions that may seems naive to most of you: does anyone know if there is...
• Isochore As Genome Coordinates ?
  Hi, In my account I have uploaded a file name iso_mm10.bed. The bed files contains coordinates o...
• Galaxy Url for Fasta and Bed index files
  Hello, What is an appropriate galaxy URL to use to obtain bed and fasta index files? I have trie...
• Stitch Maf Blocks
  Hi, I don't undestand how to use the tool "Stitch MAF blocks". I update a small bed file and now ...